ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements.

ABSTRACT: Transposable elements (TEs) produce structural variants and are considered an important source of genetic diversity. Notably, TE-gene fusion transcripts, i.e. chimeric transcripts, have been associated with adaptation in several species. However, the identification of these chimeras remains hindered due to the lack of detection tools at a transcriptome-wide scale, and to the reliance on a reference genome, even though different individuals/cells/strains have different TE insertions. Therefore, we developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts through two different modes. Mode 1 is the reference-guided approach that employs canonical genome alignment, and Mode 2 identifies chimeras derived from fixed or insertionally polymorphic TEs witho

SUBMITTER: Oliveira DS 

PROVIDER: S-EPMC10570057 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature